Todd Harris > Bio-GMOD >


Annotate this POD


New  1
Open  0
View/Report Bugs



 $ [options]

This script should be executed with superuser privileges.


Available options include (default values in parenthesis): Versions and process tasks: --version Update to the provided version (if available on the server!) --force [boolean] Force an update to the provided version (false)

 --exclude       [list...] Files, paths, or patterns to exclude from the rsync update (none)
 --help          Display this message

In order to avoid a ludicrously long incantation, full options for this script should be stored in a configuration file consisting of key=value pairs. See the "wormbase_update_defaults.cfg" file that is included with this distribution for a full description of all options complete with suitable defaults.

To invoke the script: --config /full/path/to/my.config

Controlling which update steps are executed ^

You can broadly control which steps are executed by passing either the --update_database and/or the --update_software flags.

If you would like more specific control, you can specify specific steps to run during the update by passing a comma-separated list with the "--steps" paramater. Available steps are:

  acedb         Fetch and install the acedb database
  elegans_gff   Fetch and install the C. elegans GFF database
  briggsae_gff  Fetch and install the C. briggsae GFF database
  blast         Fetch and install the blast/blat databases
  software      Rsync the software
  analyze_logs  WormBase logs; requires Analog and ReportMagic
  clear_cache   Clear the wormbase cache at /usr/local/wormbase/cache

The --update_database flag is equivalent to "--steps acedb,elegans_gff,briggsae_gff,blast,clear_cache" and the --update_software flag is equivalent "--steps software".

If the --steps option is not specified or the --update_* options are omitted, the following steps will be executed:

   acedb, elegans_gff, briggsae_gff, blast, software, clear_cache

Examples ^

Do an update of both software and databases

  ./ \
           --sync_to live \
           --update_software \

      Or more simply:

  ./ \
           --sync_to live \

Fetch the most up-to-date version of the code without updating databases:

  ./ \
           --sync_to live \

Official mirror sites should use a command like:

  ./ \
           --sync_to live \
           --update_databases \
           --update_software \
           --steps analyze_logs

Update databases without updating the software:

  ./ \
           --sync_to live \

Excluding files from the syncing process ^

If you have local files or directories stored in your WormBase distribution, you can prevent them from being overwritten by the update process by passing a space separated list of files/directories with the '--exclude' option. This options will be passed directly to rsync. See the rsync man page for more details. Note that you do NOT need to include files that contain local defaults (like as these are exluded by default.

Running under cron ^

You may wish to run this script under cron to ensure that your installation is always up-to-date.

A suggested crontab entry for a simple local installation is:

 0 2,14 * * * --sync_to live --purge 1

A suggested crontab entry for official WormBase mirror sites is:

 0 2,14 * * * --sync_to live \
        --update_databases --update_software \
        --steps analyze_logs

Crontab entries like these will check for updates twice a day -- including updating the software. Be sure to include any necessary options as well, such as the path to your mysql data directory.


None reported.


Bio::GMOD, Bio::GMOD::Update, Bio::GMOD::Update::WormBase, Bio::GMOD::Adaptor, Bio::GMOD::Adaptor::WormBase


Todd W. Harris <>.

Copyright (c) 2004-2005 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

syntax highlighting: